School of Biological Information Engineering, Jinzhou Medical University, China
Research Article
Elucidating Electronic Structure Variations in Nucleic Acid-Protein Complexes Involved in Transcription Regulation Using a Tight-Binding Approach
Author(s): Likai Du* and Chengbu Liu
Transcription Factors (TF) are proteins that regulates the transcription of genetic information from DNA to messenger RNA by binding to a specific DNA sequence. Nucleic acid-protein interactions are crucial in regulating transcription in biological systems. This work presents a quick and convenient method for constructing tight-binding models and offers physical insights into the electronic structure properties of transcription factor complexes and DNA motifs. The tight binding Hamiltonian parameters are generated using the random forest regression algorithm, which reproduces the given ab-initio level calculations with reasonable accuracy. We present a library of residue-level parameters derived from extensive electronic structure calculations over various combinations of nucleobases and amino acid side chains from high-quality DNA-protein complex structures. As an example, our approa.. View More»
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